ZCCHC12

zinc finger CCHC-type containing 12, the group of Paraneoplastic Ma antigens|Zinc fingers CCHC-type

Basic information

Region (hg38): X:118823824-118826968

Links

ENSG00000174460 ∙ NCBI:170261 ∙ OMIM:300701 ∙ HGNC:27273 ∙ Uniprot:Q6PEW1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Transcripts

Transcript IDs starting with ENST are treated as Ensembl, all others as RefSeq. Showing 4 of 5.

Transcript ID	Protein ID	Coding exons	MANE Select	MANE Plus Clinical
NM_173798.4	NP_776159.1	1	yes	-
ENST00000310164.3	ENSP00000308921.2	1	yes	-
NM_001312891.2	NP_001299820.1	1	-	-
ENST00000939481.1	ENSP00000609540.1	1	-	-

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ZCCHC12 gene.

• not_specified (39 variants)
• not_provided (8 variants)
• ZCCHC12-related_disorder (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZCCHC12 gene is commonly pathogenic or not. These statistics are base on transcript: NM_173798.4. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1	2	3
missense			37	5	1	43
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	37	6	3

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZCCHC12	protein_coding	protein_coding	ENST00000310164	1	3179

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
		125733	1	6	125740	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.683	138	162	0.849	0.0000125	2656
Missense in Polyphen		24	32.535	0.73766		678
Synonymous	-0.587	70	64.0	1.09	0.00000494	812
Loss of Function	1.39	3	6.97	0.431	5.98e-7	105

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000365	0.0000365
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000244	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.000157	0.0000980
Other	0.000221	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcriptional coactivator in the bone morphogenetic protein (BMP)-signaling pathway. It positively modulates BMP signaling by interacting with SMAD1 and associating with CBP in the transcription complex. It contributes to the BMP-induced enhancement of cholinergic-neuron-specific gene expression (By similarity). {ECO:0000250}.
• Pathway: Regulation of nuclear beta catenin signaling and target gene transcription (Consensus)

Recessive Scores

• pRec: 0.0980

Intolerance Scores

• loftool: 0.356
• rvis_EVS: -0.29
• rvis_percentile_EVS: 32.94

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.694

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Gene ontology

• Biological process: BMP signaling pathway;positive regulation of nucleic acid-templated transcription
• Cellular component: nuclear speck
• Molecular function: nucleic acid binding;protein binding;zinc ion binding;nuclear receptor transcription coactivator activity